plot_biotextgraph: plot_biotextgraph

View source: R/steps.R

plot_biotextgraphR Documentation

plot_biotextgraph

Description

Plot biotextgraph after processing graph

Usage

plot_biotextgraph(
  ret,
  edge_link = TRUE,
  edge_label = FALSE,
  show_legend = FALSE,
  cat_colors = NULL,
  query_color = "grey",
  font_family = "sans",
  colorize = FALSE,
  color_by_tag = FALSE,
  color_by_community = FALSE,
  tag_colors = NULL,
  color_text = TRUE,
  scale_range = c(5, 10),
  pal = c("blue", "red"),
  layout = "nicely",
  na_edge_color = "grey",
  add_pseudo_freq = FALSE,
  discrete_color_word = FALSE,
  use_seed = 42
)

Arguments

ret

biotext object

edge_link

whether to use edge link or edge diagonal

edge_label

whether to show edge label

show_legend

whether to show legend

cat_colors

named vector specifying color for each category of node

query_color

color for queried nodes

font_family

font family

colorize

colorize the word frequency and query separately if FALSE, no node is plotted for query nodes. it overrides color_by_tag.

color_by_tag

color by tagging information (color scale will be discrete)

color_by_community

color by community information in graph

tag_colors

palette for node color in discrete mode

color_text

whether to color the text

scale_range

scale range for node and text size

pal

palette for node color specified as (low, high)

layout

graph layout

na_edge_color

edge color for NA value

add_pseudo_freq

add pseudo value for nodes other than words

discrete_color_word

colorize words by "Words" category, not frequency.

use_seed

seed value for ggrepel

Details

Plot the network stored in biotextgraph object after processing the graph.

Value

biotext class object

See Also

plotwc plotnet

Examples

testgenes <- c("IRF3","PNKP","DDX41","ERCC1","ERCC2","XRCC1")
refseq(testgenes) |> plot_biotextgraph()

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.